Computational protocol: Warble infestations by Hypoderma tarandi (Diptera; Oestridae) recorded for the first time in West Greenland muskoxen☆

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Protocol publication

[…] In February 2012, a total of 424 muskoxen were examined post-mortem for muscle and tissue parasites at the Kangerlussuaq muskox abattoir. All muskoxen were shot in an area situated south of Kangerlussuaq (66°15’N-67°N) () where hunting of muskoxen occurs twice yearly: January–March and August–October.During slaughter, the hides were removed quickly without the possibility of inspection of the subcutaneous tissues, but the carcasses were subsequently examined for warble lesions. The warble larvae recovered were stored in 70% ethanol and sent to the University of Copenhagen. After morphological examination, DNA extraction was performed using a commercial kit (Epicentre Biotechnologies Complete DNA and RNA Purification Kit) following the Total Nucleic Acids Purification Protocols for tissue samples.A part of the mitochondrial gene encoding for subunit I of cytochrome oxidase (COI) was amplified by PCR using the primers UEA7 5′-TAC AGT TGG AAT AGA CGT TGA TAC-3′ and UEA10 5′-TCC AAT GCA CTA ATC TGC CAT ATT A-3′ (). This region has been shown to contain sufficient variability among Hypoderma spp. for species identification (). After enzymatic purification, the PCR products were sequenced in both directions by Macrogen (Seoul, Korea).The genetic relationship between the unknown Hypoderma species were compared to H. bovis (AF497761), H. lineatum (AF497762), H. diana (AF497763), H. tarandi (AF497764), H. actaeon (AF497765), and H. sinense (AY350769) using Dermatobia hominis (AY463155) as an out group. Sequences were analyzed by Neighbour-Joining (NJ) and Minimum Evolution (ME) tree methods using Kimura-2-parameter distance and by Maximum Parsimony where the tree was obtained using the Close-Neighbor-Interchange algorithm. The robustness of the topology was assessed with 1000 bootstraps. The analysis was done using MEGA version 5 (). […]

Pipeline specifications

Software tools MUSCLE, MEGA
Application Nucleotide sequence alignment
Organisms Rangifer tarandus, Homo sapiens
Diseases Tick Infestations